FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: N6KLQ

Calculation Name: 1AP8-A-Other549

Preferred Name:

Target Type:

Ligand Name: 7n-methyl-8-hydroguanosine-5'-diphosphate

Ligand 3-letter code: M7G

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AP8

Chain ID: A

ChEMBL ID:

UniProt ID: P07260

Base Structure: SolutionNMR

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2406072.604283
FMO2-HF: Nuclear repulsion 2322608.614749
FMO2-HF: Total energy -83463.989533
FMO2-MP2: Total energy -83713.896725


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-79.454-77.390.04-0.753-1.351-0.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.906
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3VAL0-0.033-0.0223.1500.1522.2160.040-0.753-1.351-0.002
4A4GLU-1-0.869-0.9285.749-28.940-28.9400.0000.0000.0000.000
5A5GLU-1-0.962-0.9719.590-20.351-20.3510.0000.0000.0000.000
6A6VAL0-0.043-0.02812.7250.2910.2910.0000.0000.0000.000
7A7SER0-0.0030.00415.4311.1011.1010.0000.0000.0000.000
8A8LYS10.9640.98218.32314.86014.8600.0000.0000.0000.000
9A9LYS10.9680.98119.97413.42313.4230.0000.0000.0000.000
10A10PHE0-0.038-0.03323.413-0.273-0.2730.0000.0000.0000.000
11A11GLU-1-0.941-0.98825.751-9.939-9.9390.0000.0000.0000.000
12A12GLU-1-0.918-0.93428.668-10.678-10.6780.0000.0000.0000.000
13A13ASN0-0.045-0.01830.654-0.055-0.0550.0000.0000.0000.000
14A14VAL00.0320.01033.4700.2520.2520.0000.0000.0000.000
15A15SER0-0.049-0.02435.9130.0880.0880.0000.0000.0000.000
16A16VAL0-0.042-0.03437.5600.1330.1330.0000.0000.0000.000
17A17ASP-1-0.947-0.95838.789-7.903-7.9030.0000.0000.0000.000
18A18ASP-1-0.872-0.93039.962-7.595-7.5950.0000.0000.0000.000
19A19THR0-0.038-0.02135.501-0.294-0.2940.0000.0000.0000.000
20A20THR00.0410.00935.879-0.089-0.0890.0000.0000.0000.000
21A21ALA0-0.0160.00931.901-0.004-0.0040.0000.0000.0000.000
22A22THR00.004-0.00433.655-0.129-0.1290.0000.0000.0000.000
23A23PRO0-0.067-0.03133.077-0.082-0.0820.0000.0000.0000.000
24A24LYS10.8810.93726.00111.63711.6370.0000.0000.0000.000
25A25THR00.0870.04830.349-0.189-0.1890.0000.0000.0000.000
26A26VAL0-0.019-0.01325.424-0.353-0.3530.0000.0000.0000.000
27A27LEU00.012-0.01427.333-0.359-0.3590.0000.0000.0000.000
28A28SER0-0.053-0.02030.0020.1730.1730.0000.0000.0000.000
29A29ASP-1-0.889-0.93433.170-8.953-8.9530.0000.0000.0000.000
30A30SER0-0.049-0.05234.7050.0000.0000.0000.0000.0000.000
31A31ALA0-0.0230.00837.7870.2230.2230.0000.0000.0000.000
32A32HIS00.0060.01038.2830.2590.2590.0000.0000.0000.000
33A33PHE0-0.013-0.01642.0640.0990.0990.0000.0000.0000.000
34A34ASP-1-0.878-0.92642.706-7.450-7.4500.0000.0000.0000.000
35A35VAL00.0070.01145.8810.1600.1600.0000.0000.0000.000
36A36LYS10.8660.91847.8596.7686.7680.0000.0000.0000.000
37A37HIS00.0670.02143.8750.1440.1440.0000.0000.0000.000
38A38PRO0-0.0210.00442.2780.0050.0050.0000.0000.0000.000
39A39LEU0-0.0130.01843.5890.1340.1340.0000.0000.0000.000
40A40ASN00.0310.01540.923-0.013-0.0130.0000.0000.0000.000
41A41THR00.0180.00040.011-0.274-0.2740.0000.0000.0000.000
42A42LYS10.8540.93234.6468.9978.9970.0000.0000.0000.000
43A43TRP00.002-0.01239.4930.0280.0280.0000.0000.0000.000
44A44THR0-0.028-0.02339.706-0.127-0.1270.0000.0000.0000.000
45A45LEU00.0180.01942.4370.1360.1360.0000.0000.0000.000
46A46TRP0-0.019-0.00440.466-0.066-0.0660.0000.0000.0000.000
47A47TYR00.0200.01046.9590.1500.1500.0000.0000.0000.000
48A48THR00.004-0.00650.637-0.073-0.0730.0000.0000.0000.000
49A49LYS10.9190.95153.0845.8305.8300.0000.0000.0000.000
50A50PRO00.0310.02354.5320.1290.1290.0000.0000.0000.000
51A51ALA00.014-0.01756.548-0.040-0.0400.0000.0000.0000.000
52A52VAL0-0.050-0.01657.0000.0980.0980.0000.0000.0000.000
53A53ASP-1-0.784-0.89553.953-5.997-5.9970.0000.0000.0000.000
54A54LYS10.8870.93555.7165.1755.1750.0000.0000.0000.000
55A55SER0-0.078-0.03657.5370.0940.0940.0000.0000.0000.000
56A56GLU-1-0.931-0.96153.274-5.876-5.8760.0000.0000.0000.000
57A57SER00.029-0.02449.523-0.061-0.0610.0000.0000.0000.000
58A58TRP0-0.059-0.04348.6390.1050.1050.0000.0000.0000.000
59A59SER0-0.008-0.01545.9600.0240.0240.0000.0000.0000.000
60A60ASP-1-0.884-0.89047.247-6.741-6.7410.0000.0000.0000.000
61A61LEU0-0.147-0.06049.3710.0790.0790.0000.0000.0000.000
62A62LEU0-0.044-0.02147.3530.0240.0240.0000.0000.0000.000
63A63ARG10.9590.98147.0306.5836.5830.0000.0000.0000.000
64A64PRO0-0.002-0.00942.2710.0570.0570.0000.0000.0000.000
65A65VAL0-0.015-0.02743.095-0.081-0.0810.0000.0000.0000.000
66A66THR0-0.0130.00542.450-0.181-0.1810.0000.0000.0000.000
67A67SER0-0.067-0.04438.9140.0220.0220.0000.0000.0000.000
68A68PHE0-0.0120.00938.637-0.284-0.2840.0000.0000.0000.000
69A69GLN00.0570.02137.1890.0530.0530.0000.0000.0000.000
70A70THR0-0.047-0.02141.5840.0390.0390.0000.0000.0000.000
71A71VAL00.0970.04344.9350.0230.0230.0000.0000.0000.000
72A72GLU-1-0.931-0.96247.837-6.234-6.2340.0000.0000.0000.000
73A73GLU-1-0.888-0.95444.766-6.982-6.9820.0000.0000.0000.000
74A74PHE00.0180.00047.8890.0700.0700.0000.0000.0000.000
75A75TRP0-0.015-0.01349.6010.1340.1340.0000.0000.0000.000
76A76ALA00.0290.01450.3570.1300.1300.0000.0000.0000.000
77A77ILE0-0.059-0.02649.3970.0820.0820.0000.0000.0000.000
78A78ILE00.0200.00653.3360.1180.1180.0000.0000.0000.000
79A79GLN00.0180.01553.0590.1340.1340.0000.0000.0000.000
80A80ASN0-0.129-0.06055.1700.0130.0130.0000.0000.0000.000
81A81ILE00.0340.03358.3090.0710.0710.0000.0000.0000.000
82A82PRO0-0.032-0.00657.4830.0780.0780.0000.0000.0000.000
83A83GLU-1-0.826-0.96056.490-5.588-5.5880.0000.0000.0000.000
84A84PRO0-0.0170.02160.7880.0680.0680.0000.0000.0000.000
85A85HIS0-0.101-0.08964.0330.0730.0730.0000.0000.0000.000
86A86GLU-1-0.876-0.92363.761-4.893-4.8930.0000.0000.0000.000
87A87LEU0-0.0340.01459.582-0.025-0.0250.0000.0000.0000.000
88A88PRO0-0.041-0.02061.4970.0840.0840.0000.0000.0000.000
89A89LEU0-0.044-0.05563.5660.0210.0210.0000.0000.0000.000
90A90LYS10.8780.93560.2695.1005.1000.0000.0000.0000.000
91A91SER00.0710.04157.332-0.055-0.0550.0000.0000.0000.000
92A92ASP-1-0.833-0.90753.923-5.820-5.8200.0000.0000.0000.000
93A93TYR0-0.0350.00751.999-0.122-0.1220.0000.0000.0000.000
94A94HIS10.8280.93048.3836.3956.3950.0000.0000.0000.000
95A95VAL00.0530.04245.757-0.104-0.1040.0000.0000.0000.000
96A96PHE00.0180.02043.7320.0910.0910.0000.0000.0000.000
97A97ARG10.9020.93234.7238.5478.5470.0000.0000.0000.000
98A98ASN0-0.0060.04339.372-0.328-0.3280.0000.0000.0000.000
99A99ASP-1-0.888-0.92239.374-8.074-8.0740.0000.0000.0000.000
100A100VAL0-0.0010.02039.105-0.206-0.2060.0000.0000.0000.000
101A101ARG10.8510.93435.8078.3338.3330.0000.0000.0000.000
102A102PRO0-0.0190.00740.806-0.060-0.0600.0000.0000.0000.000
103A103GLU-1-0.738-0.88342.038-7.055-7.0550.0000.0000.0000.000
104A104TRP0-0.077-0.05345.8220.1040.1040.0000.0000.0000.000
105A105GLU-1-0.886-0.93746.895-6.341-6.3410.0000.0000.0000.000
106A106ASP-1-0.891-0.95543.502-7.308-7.3080.0000.0000.0000.000
107A107GLU-1-0.810-0.93544.636-7.221-7.2210.0000.0000.0000.000
108A108ALA00.0070.01546.1570.0150.0150.0000.0000.0000.000
109A109ASN0-0.033-0.03940.985-0.016-0.0160.0000.0000.0000.000
110A110ALA0-0.023-0.01043.174-0.153-0.1530.0000.0000.0000.000
111A111LYS10.9000.96342.6817.3127.3120.0000.0000.0000.000
112A112GLY00.0750.05346.5860.0630.0630.0000.0000.0000.000
113A113GLY0-0.101-0.05749.5190.1190.1190.0000.0000.0000.000
114A114LYS10.8980.96451.1095.9805.9800.0000.0000.0000.000
115A115TRP0-0.016-0.01653.6700.1220.1220.0000.0000.0000.000
116A116SER0-0.016-0.02756.206-0.072-0.0720.0000.0000.0000.000
117A117PHE00.0110.00256.9650.0930.0930.0000.0000.0000.000
118A118GLN00.0300.02261.955-0.048-0.0480.0000.0000.0000.000
119A119LEU00.0530.02064.7550.1050.1050.0000.0000.0000.000
120A120ARG10.8070.90066.7714.4804.4800.0000.0000.0000.000
121A121GLY0-0.0150.00169.9970.0480.0480.0000.0000.0000.000
122A122LYS10.9450.96369.9384.3804.3800.0000.0000.0000.000
123A123GLY00.0320.00369.5070.0630.0630.0000.0000.0000.000
124A124ALA0-0.029-0.01668.1330.0290.0290.0000.0000.0000.000
125A125ASP-1-0.728-0.83265.752-4.794-4.7940.0000.0000.0000.000
126A126ILE0-0.050-0.01263.819-0.040-0.0400.0000.0000.0000.000
127A127ASP-1-0.788-0.93060.359-5.271-5.2710.0000.0000.0000.000
128A128GLU-1-0.845-0.92459.453-5.304-5.3040.0000.0000.0000.000
129A129LEU0-0.059-0.01959.162-0.089-0.0890.0000.0000.0000.000
130A130TRP00.0030.00657.145-0.051-0.0510.0000.0000.0000.000
131A131LEU00.0120.00254.507-0.099-0.0990.0000.0000.0000.000
132A132ARG10.9610.98054.7695.3915.3910.0000.0000.0000.000
133A133THR0-0.018-0.00454.833-0.063-0.0630.0000.0000.0000.000
134A134LEU0-0.029-0.02552.913-0.102-0.1020.0000.0000.0000.000
135A135LEU0-0.022-0.01750.429-0.135-0.1350.0000.0000.0000.000
136A136ALA00.0270.01949.700-0.149-0.1490.0000.0000.0000.000
137A137VAL0-0.016-0.01049.938-0.114-0.1140.0000.0000.0000.000
138A138ILE0-0.100-0.03645.697-0.143-0.1430.0000.0000.0000.000
139A139GLY00.020-0.02545.392-0.225-0.2250.0000.0000.0000.000
140A140GLU-1-0.928-0.96646.401-6.108-6.1080.0000.0000.0000.000
141A141THR0-0.070-0.03845.5890.0960.0960.0000.0000.0000.000
142A142ILE0-0.040-0.00847.7290.0840.0840.0000.0000.0000.000
143A143ASP-1-0.879-0.93247.474-6.729-6.7290.0000.0000.0000.000
144A144GLU-1-1.059-1.03749.565-5.717-5.7170.0000.0000.0000.000
145A145ASP-1-0.902-0.96850.127-6.069-6.0690.0000.0000.0000.000
146A146ASP-1-0.818-0.91246.049-7.083-7.0830.0000.0000.0000.000
147A147SER0-0.0300.00144.543-0.147-0.1470.0000.0000.0000.000
148A148GLN0-0.050-0.03045.179-0.216-0.2160.0000.0000.0000.000
149A149ILE0-0.021-0.00647.8700.0280.0280.0000.0000.0000.000
150A150ASN0-0.051-0.05143.937-0.100-0.1000.0000.0000.0000.000
151A151GLY0-0.025-0.03244.784-0.180-0.1800.0000.0000.0000.000
152A152VAL00.0020.01947.2620.1540.1540.0000.0000.0000.000
153A153VAL0-0.005-0.01749.941-0.108-0.1080.0000.0000.0000.000
154A154LEU00.0060.02052.5980.1220.1220.0000.0000.0000.000
155A155SER0-0.006-0.02255.495-0.077-0.0770.0000.0000.0000.000
156A156ILE0-0.0220.03557.8410.1170.1170.0000.0000.0000.000
157A157ARG10.9290.94558.4885.3875.3870.0000.0000.0000.000
158A158LYS10.9770.98163.9784.6434.6430.0000.0000.0000.000
159A159GLY0-0.030-0.01367.5150.0480.0480.0000.0000.0000.000
160A160GLY0-0.008-0.01967.1150.0670.0670.0000.0000.0000.000
161A161ASN0-0.0250.01063.055-0.034-0.0340.0000.0000.0000.000
162A162LYS10.8770.91860.5475.2565.2560.0000.0000.0000.000
163A163PHE00.0010.02557.867-0.082-0.0820.0000.0000.0000.000
164A164ALA00.004-0.03454.4570.0450.0450.0000.0000.0000.000
165A165LEU00.0070.02751.842-0.040-0.0400.0000.0000.0000.000
166A166TRP0-0.051-0.02048.3030.0750.0750.0000.0000.0000.000
167A167THR00.0670.03348.818-0.131-0.1310.0000.0000.0000.000
168A168LYS10.9160.96341.5067.6367.6360.0000.0000.0000.000
169A169SER0-0.037-0.04745.862-0.097-0.0970.0000.0000.0000.000
170A170GLU-1-0.867-0.95347.871-6.095-6.0950.0000.0000.0000.000
171A171ASP-1-0.814-0.89850.617-5.873-5.8730.0000.0000.0000.000
172A172LYS10.9230.94053.1095.8165.8160.0000.0000.0000.000
173A173GLU-1-0.927-0.94956.525-5.520-5.5200.0000.0000.0000.000
174A174PRO0-0.064-0.02454.0260.1470.1470.0000.0000.0000.000
175A175LEU00.1040.07053.2690.0850.0850.0000.0000.0000.000
176A176LEU0-0.050-0.02256.9510.0870.0870.0000.0000.0000.000
177A177ARG10.9150.96158.2655.5775.5770.0000.0000.0000.000
178A178ILE00.0520.04254.6690.1220.1220.0000.0000.0000.000
179A179GLY00.0280.01058.8610.0560.0560.0000.0000.0000.000
180A180GLY0-0.030-0.01160.3470.0830.0830.0000.0000.0000.000
181A181LYS10.9220.94160.4925.4195.4190.0000.0000.0000.000
182A182PHE00.0360.00455.2450.0990.0990.0000.0000.0000.000
183A183LYS10.9360.97861.1864.8844.8840.0000.0000.0000.000
184A184GLN0-0.029-0.01964.3000.0680.0680.0000.0000.0000.000
185A185VAL00.0040.01060.8550.0710.0710.0000.0000.0000.000
186A186LEU0-0.025-0.01161.5230.0230.0230.0000.0000.0000.000
187A187LYS10.8210.88965.1384.7814.7810.0000.0000.0000.000
188A188LEU0-0.100-0.02267.1800.0740.0740.0000.0000.0000.000
189A189THR0-0.032-0.03570.0300.0290.0290.0000.0000.0000.000
190A190ASP-1-0.885-0.95872.629-4.413-4.4130.0000.0000.0000.000
191A191ASP-1-0.839-0.90572.436-4.347-4.3470.0000.0000.0000.000
192A192GLY0-0.021-0.01769.753-0.049-0.0490.0000.0000.0000.000
193A193HIS10.8960.92266.8214.7164.7160.0000.0000.0000.000
194A194LEU0-0.039-0.01562.072-0.052-0.0520.0000.0000.0000.000
195A195GLU-1-0.902-0.91459.201-5.392-5.3920.0000.0000.0000.000
196A196PHE0-0.0120.00759.196-0.088-0.0880.0000.0000.0000.000
197A197PHE00.043-0.00756.8240.0550.0550.0000.0000.0000.000
198A198PRO00.0300.03353.886-0.088-0.0880.0000.0000.0000.000
199A199HIS00.0580.01749.3390.0700.0700.0000.0000.0000.000
200A200SER00.0210.01151.419-0.009-0.0090.0000.0000.0000.000
201A201SER0-0.086-0.07153.4160.0440.0440.0000.0000.0000.000
202A202ALA00.0130.01650.6030.0830.0830.0000.0000.0000.000
203A203ASN00.0200.02148.2510.0220.0220.0000.0000.0000.000
204A204GLY00.0540.02950.947-0.023-0.0230.0000.0000.0000.000
205A205ARG10.8950.97953.9785.3645.3640.0000.0000.0000.000
206A206HIS0-0.005-0.01456.6880.1000.1000.0000.0000.0000.000
207A207PRO0-0.0270.00255.7500.0960.0960.0000.0000.0000.000
208A208GLN00.032-0.00459.002-0.041-0.0410.0000.0000.0000.000
209A209PRO0-0.025-0.00258.740-0.073-0.0730.0000.0000.0000.000
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